pyproject.toml

# https://peps.python.org/pep-0517/
[build-system]
requires = ["hatchling", "hatch-vcs"]
build-backend = "hatchling.build"

# https://hatch.pypa.io/latest/config/metadata/
[tool.hatch.version]
source = "vcs"

# read more about configuring hatch at:
# https://hatch.pypa.io/latest/config/build/
[tool.hatch.build.targets.wheel]
only-include = ["src"]
sources = ["src"]

# https://peps.python.org/pep-0621/
[project]
name = "cellier"
dynamic = ["version"]
description = "A workshop for rendering cellular models."
readme = "README.md"
requires-python = ">=3.10"
license = { text = "BSD-3-Clause" }
authors = [{ name = "Kevin Yamauchi", email = "kevin.yamauchi@gmail.com" }]
# https://pypi.org/classifiers/
classifiers = [
    "Development Status :: 3 - Alpha",
    "License :: OSI Approved :: BSD License",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Typing :: Typed",
]
# add your package dependencies here
dependencies = [
    "cmap>=0.6.0",
    "einops>=0.8.1",
    "numpy<2.5.0",
    "psygnal",
    "pydantic",
    "pygfx>=0.17.0",
    "pylinalg>=0.6.7",
    "qtpy",
    "rendercanvas>=2.7.1",
    "scipy>=1.15.2",
    "superqt>=0.7.2",
    "tensorstore>=0.1.74",
    "yaozarrs>=0.2",
    "zarr",
]

# https://peps.python.org/pep-0621/#dependencies-optional-dependencies
# "extras" (e.g. for `pip install .[test]`)
[project.optional-dependencies]
remote = [
    "yaozarrs[io]>=0.2",   # includes fsspec for S3/GCS/HTTP metadata reading
]
pyside = ["PySide6"]
pyqt = ["PyQt6"]
# anywidget front-end (notebook hosts: Jupyter, marimo).  ipywidgets and
# rendercanvas arrive transitively (via anywidget and pygfx respectively); the
# notebook host applications (jupyter, marimo) are not declared here -- the user
# installs whichever host they run in.
anywidget = ["anywidget", "simplejpeg", "sidecar"]
# spatial graph support: geff file reading and the "roi" slice strategy.
# Both are lazily imported; the default "mask" slice path needs neither.
graph = ["geff", "spatial-graph"]
test = [
    "pytest",
    "pytest-asyncio",
    "pytest-cov",
    "pytest-qt",
    # so CI exercises the geff loader and the "roi" slice strategy; without
    # it those tests would silently skip and only "mask" would ever run.
    "cellier[graph]",
]
# add anything else you like to have in your dev environment here
dev = [
    "ipython",
    "marimo",
    "pdbpp",  # https://github.com/pdbpp/pdbpp
    "pre-commit",
    "rich",  # https://github.com/Textualize/rich
    "ruff",
    "zensical>=0.0.40",
    "mkdocstrings-python",
    "griffe-pydantic>=1.3.1",
]

# optional rich-powered debug logging
logging = ["rich>=13.0"]

# dependencies for the example scripts
examples = ["scikit-image", "pyvista"]

# get all dependencies for development
dev-all = ["cellier[dev,test,pyside,examples,logging,remote,anywidget]"]

[project.urls]
homepage = "https://github.com/kevinyamauchi/cellier"
repository = "https://github.com/kevinyamauchi/cellier"

# Entry points
# https://peps.python.org/pep-0621/#entry-points
# same as console_scripts entry point
# [project.scripts]
# cellier-cli = "cellier:main_cli"

# [project.entry-points."some.group"]
# tomatoes = "cellier:main_tomatoes"

# https://docs.astral.sh/ruff
[tool.ruff]
line-length = 88
target-version = "py38"
src = ["src"]

# https://docs.astral.sh/ruff/rules
[tool.ruff.lint]
pydocstyle = { convention = "numpy" }
select = [
    "E",    # style errors
    "W",    # style warnings
    "F",    # flakes
    "D",    # pydocstyle
    "D417", # Missing argument descriptions in Docstrings
    "I",    # isort
    "UP",   # pyupgrade
    "C4",   # flake8-comprehensions
    "B",    # flake8-bugbear
    "A001", # flake8-builtins
    "RUF",  # ruff-specific rules
    "TCH",  # flake8-type-checking
    "TID",  # flake8-tidy-imports
]
ignore = [
    "D401",  # First line should be in imperative mood (remove to opt in)
]

[tool.ruff.lint.per-file-ignores]
"tests/*.py" = ["D", "S"]
"scripts/**/*.py" = ["D", "E402", "E501", "E702", "F841", "F821", "TCH", "RUF001", "RUF002", "RUF003", "RUF006", "B007", "C416"]
# Pydantic v2 models require these imports at runtime for field type resolution
"src/cellier/scene/*.py" = ["TCH001", "TCH003"]
"src/cellier/viewer_model.py" = ["TCH001", "TCH003"]
"src/cellier/visuals/_base_visual.py" = ["TCH001", "TCH003"]
"src/cellier/data/graph/*.py" = ["TCH001", "TCH003"]
# docstring-code-format collapses wrapped examples; E501 fires on indent+content
"src/cellier/gui/**/*.py" = ["E501"]

# https://docs.astral.sh/ruff/formatter/
[tool.ruff.format]
docstring-code-format = true
skip-magic-trailing-comma = false  # default is false

# https://docs.pytest.org/
[tool.pytest.ini_options]
minversion = "7.0"
testpaths = ["tests"]
filterwarnings = [
    "error",
    "ignore:'asyncio.AbstractEventLoopPolicy':DeprecationWarning",
    # spatial_graph -> witty -> Cheetah -> `import cgi`.  Cheetah guards that
    # import with `except ImportError` for Python 3.13, where cgi was removed,
    # but on 3.11/3.12 cgi still exists and only warns -- and a try/except
    # cannot catch a warning.  Fires once per process, on whichever test first
    # builds a SpatialGraph, so it cannot be pinned to one test module.
    # Drop this when Cheetah stops importing cgi, or when 3.11 and 3.12 leave
    # the CI matrix.
    "ignore:'cgi' is deprecated:DeprecationWarning",
]
asyncio_mode = "auto"
asyncio_default_fixture_loop_scope = "function"

# https://coverage.readthedocs.io/
[tool.coverage.report]
show_missing = true
exclude_lines = [
    "pragma: no cover",
    "if TYPE_CHECKING:",
    "@overload",
    "except ImportError",
    "\\.\\.\\.",
    "raise NotImplementedError()",
    "pass",
]

[tool.coverage.run]
source = ["cellier"]

# https://github.com/mgedmin/check-manifest#configuration
# add files that you want check-manifest to explicitly ignore here
# (files that are in the repo but shouldn't go in the package)
[tool.check-manifest]
ignore = [
    ".pre-commit-config.yaml",
    ".ruff_cache/**/*",
    "tests/**/*",
]

[tool.typos.default.extend-words]
# LOD = Level Of Detail — not a typo for "load"
lod = "lod"
# ser = serialization abbreviation (pydantic_core API uses _ser_schema suffixes)
ser = "ser"
# nd = number of dimensions abbreviation (used as local variable)
nd = "nd"
dims = "dims"